Spread of Gamma (P.1) sub-lineages carrying Spike mutations close to the furin cleavage site and deletions in the N-terminal domain drives ongoing transmission of SARS-CoV-2 in Amazonas, Brazil

Abstract

The Amazonas was one of the most heavily affected Brazilian states by the COVID-19 epidemic. Despite a large number of infected people, particularly during the second wave associated with the spread of the Variant of Concern (VOC) Gamma (lineage P.1), SARS-CoV-2 continues to circulate in the Amazonas. To understand how SARS-CoV-2 persisted in a human population with a high immunity barrier, we generated 1,188 SARS-CoV-2 whole-genome sequences from individuals diagnosed in the Amazonas state from 1st January to 6th July 2021, of which 38 were vaccine breakthrough infections. Our study reveals a sharp increase in the relative prevalence of Gamma plus (P.1+) variants, designated as Pango Lineages P.1.3 to P.1.6, harboring two types of additional Spike changes: deletions in the N-terminal (NTD) domain (particularly 𝚫144 or 𝚫141-144) associated with resistance to anti-NTD neutralizing antibodies or mutations at the S1/S2 junction (N679K or P681H) that probably enhance the binding affinity to the furin cleavage site, as suggested by our molecular dynamics simulations. As lineages P.1.4 (S:N679K) and P.1.6 (S:P681H) expanded (Re > 1) from March to July 2021, the lineage P.1 declined (Re < 1) and the median Ct value of SARS-CoV-2 positive cases in Amazonas significantly decreases. Still, we found no overrepresentation of P.1+ variants among breakthrough cases of fully vaccinated patients (71%) in comparison to unvaccinated individuals (93%). This evidence supports that the ongoing endemic transmission of SARS-CoV-2 in the Amazonas is driven by the spread of new local Gamma/P.1 sub-lineages that are more transmissible, although not more efficient to evade vaccine-elicited immunity than the parental VOC. Finally, as SARS-CoV-2 continues to spread in human populations with a declining density of susceptible hosts, the risk of selecting new variants with higher infectivity are expected to increase.

Phylogenetic-based inference reveals distinct transmission dynamics of SARS-CoV-2 variant of concern Gamma and lineage P.2 in Brazil

“…To estimate the precise onset date of the lineage P.2 and the VOC Gamma, we first excluded all P.1 or P.2 sequences that did not display the full set of variant-defining mutations and those recently classified as Gamma-like 14 . Next, we assessed the temporal signal of the P.2 and Gamma datasets and excluded several outliers, including some of the sequences with the earliest recorded sampling dates ( Fig 2a ).…”

“…The viral RNA was subjected to reverse transcription and PCR amplification using in-house protocols developed by COVID-19 Fiocruz Genomic Network 19,20 or the Illumina COVIDSeq Test (Illumina), including some primers to cover regions with dropout 14 . Normalized pooled amplicons of each sample were used to prepare NGS libraries with Nextera XT (FC-131-1096) and clustered with MiSeq Reagent Kit v2 (500-cycles - MS-102-2003) on 2 × 250 cycles (in-house protocols) or 2 × 150 cycles (MS-103-1002) paired-end runs.…”

“…To estimate the precise onset date of the lineage P.2 and the VOC Gamma, we first excluded all P.1 or P.2 sequences that did not display the full set of variant-defining mutations and those recently classified as Gamma-like 14 . Next, we assessed the temporal signal of the P. is the author/funder, who has granted medRxiv a license to display the preprint in (which was not certified by peer review) To describe the pathways that shaped the country-wide dissemination of the lineage P.2 and the VOC Gamma in Brazil, we performed a discrete Bayesian phylogeographic reconstruction.…”

Re-emergence of Gamma-like-II and emergence of Gamma-S:E661D SARS-CoV-2 lineages in the south of Brazil after the 2021 outbreak

“…Our results reinforce the importance of genomic vigilance to track possible novel VOIs that may arise from the current scenario of low vaccination rates and uncontrolled dissemination of SARS-CoV-2 in Brazil, as previously documented [ 39 ]. In addition, there are currently 11 Gamma sublines that are accumulating new mutations near the furin cleavage site, among them the E661D described in this work [ 40 ].…”

Genomic Surveillance of SARS-CoV-2 Lineages Indicates Early Circulation of P.1 (Gamma) Variant of Concern in Southern Brazil

“…The P.1 lineage-defining mutations in the Spike protein, especially in the receptor-binding domains (RBD) such as K417T, E484K and N501Y, are of concern because they may enhance ACE2 affinity and contribute to antibody evasion ( 10 ). Recently, new sublineages (P.1.2 to P.1.8) that have emerged from P.1 have been reported in Brazil ( 11 , 12 ), which indicates a continuous evolution of the virus and the community spread in the country.…”